Merge pull request #142 from automl/development

Version 1.2

Author: sarah-segel

.flake8

@@ -6,5 +6,7 @@ extend-exclude =
     .venv
     build
 extend-ignore =
-    E203  # No whitespace before ':' in [x : y]
-    E731  # No lambdas — too strict
+    # No whitespace before ':' in [x : y]
+    E203,
+    # No lambdas — too strict
+    E731,

.github/workflows/docs.yml

@@ -1,5 +1,9 @@
 name: docs
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
 on:
   # Trigger manually
   workflow_dispatch:
@@ -22,19 +26,22 @@ env:
 jobs:
   build-and-deploy:
     runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash # Default to using bash on all
     steps:
     - name: Checkout
-      uses: actions/checkout@v2
+      uses: actions/checkout@v4
 
     - name: Setup Python
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
         python-version: 3.9
 
     - name: Install dependencies
       run: |
         pip install .
-        pip install .[dev]
+        pip install ".[dev]"
 
     - name: Make docs
       run: |

.github/workflows/pytest.yml

@@ -1,25 +1,50 @@
 name: tests
-on: [ push ]
+
+# Cancel previous tests for this branch if a new commit is pushed
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+on:
+  # Allow manual trigger of workflow
+  workflow_dispatch:
+
+  # Run tests on push/merge to main
+  push:
+    branches:
+      - main
+
+  # Run tests on anything that has a pull request to main/development
+  pull_request:
+    branches:
+      - main
+      - development
+
 jobs:
   pytest:
-    name: PyTest
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v2
-      - name: Add conda to system path
-        run: |
-          # $CONDA is an environment variable pointing to the root of the miniconda directory
-          echo $CONDA/bin >> $GITHUB_PATH
+    name: Test ${{ matrix.python-version }}-${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    defaults:
+      run:
+        shell: bash # Default to using bash on all
+
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.9", "3.10"] # "3.11" fails due to swig
+        os: ["ubuntu-latest"] # "macos-latest", "windows-latest" fails due to swig
 
+    steps:
+      - uses: actions/checkout@v4
       - name: Setup Python 3.9
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v5
         with:
-          python-version: 3.9
+          python-version: ${{ matrix.python-version }}
 
       - name: Install dependencies
         run: |
-          conda install -c anaconda swig
-          make install-dev
-          
-      - name: Run pytest 
+          pip install swig
+          python -m pip install ".[dev]"
+
+      - name: Run pytest
         run: pytest tests

.pre-commit-config.yaml

@@ -14,7 +14,7 @@ repos:
         files: tests
 
   - repo: https://github.com/ambv/black
-    rev: 23.1.0
+    rev: 23.3.0
     hooks:
       - id: black
         name: black formatter deepcave
@@ -33,14 +33,38 @@ repos:
     hooks:
       - id: pydocstyle
         files: deepcave
-        additional_dependencies: ["toml"] # Needed to parse pyproject.toml
+        additional_dependencies: ["tomli"] # Needed to parse pyproject.toml
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v0.930
+    rev: v1.5.1
     hooks:
       - id: mypy
         name: mypy deepcave
         files: deepcave
+        args: [--install-types, --non-interactive]
+        additional_dependencies: [
+            'wheel>=0.41.2',
+            'setuptools==68.2.2',
+            'absl-py>=1.0.0',
+            'jsonlines>=3.0.0',
+            'pandas>=1.3.4',
+            'numpy>=1.22.2',
+            'matplotlib>=3.5.1',
+            'pyyaml>=6.0.1',
+            'kaleido>=0.2.1',
+            'gplearn>=0.4.2',
+            'sympy>=1.12',
+            'ConfigSpace==0.6.1',
+            'pyrfr>=0.9.0',
+            'hpbandster==0.7.4',
+            'dash==2.0.0',
+            'dash-extensions==0.0.71',
+            'dash-bootstrap-components==1.0.3',
+            'redis>=4.1.4',
+            'rq>=1.10.1',
+            'werkzeug==2.0.3',
+            'pyPDPPartitioner>=0.1.8'
+        ] # Needed for mypy, so that it knows the types to check
 
   - repo: https://github.com/PyCQA/flake8
     rev: 6.0.0

CHANGELOG.md

@@ -1,3 +1,66 @@
+# Version 1.2
+
+## Plugins
+- Add symbolic explanations plugin (#46).
+- It is now possible to view multiple unequal runs at once in Cost over Time and Pareto (#93).
+- Runs with unequal objectives cannot be displayed together.
+- Added an enum for displaying according warning messages.
+
+## Enhancements
+- Fix lower bounds of dependency versions.
+- Allow to load multi-objective SMAC3v2 and add example (#69).
+- Allow to load runs with multiple seeds and add examples (#70).
+- Correct incumbent calculation when single objective should be maximized.
+- Correct range of configuration cube slider for number of configs.
+- Do not disable existing loggers.
+- Update author email.
+- Add exit button which first deletes running jobs and then terminates DeepCave.
+- Nicer handling of Keyboard Interrupt.
+- Disable debug mode.
+- Save plotly plots in higher resolution upon download.
+- Get hovertext per budget in Footprint, Config Cube, Cost over Time, and Pareto Front.
+
+## Bug-Fixes
+- Fix missing objective specification in LPI evaluator (#71).
+- Don't convert BOHB runs with status 'running' (consistent with SMAC).
+- Fix api examples (#68).
+- Reset inputs to fix error when subsequently selecting runs with different configspaces, objectives or budgets (#106).
+- Fix errors due to changing inputs before runselection (#64).
+- For fANOVA, remove constant hyperparameters from configspace (#9).
+- When getting budget, objectives etc from multiple runs in Cost over Time and Pareto Front:
+    - Instead of taking the first run as comparative value,
+    - take the one with the lowest budget, else the index for the budgets could be out of bounds.
+- For PCP, show hyperparameters with highest importance closest to the cost, i.e. right (#124).
+- Add init files to all test directories.
+- Correct LPI importance tests.
+- Free port when exiting via the exit button (#52).
+
+## Documentation
+- Add How to Contribute section.
+- Expand documentation for partial dependence plugin.
+
+## Version-Updates
+- Black version from 23.1.0 to 23.3.0
+- Mypy from 0.930 to 1.5.1
+
+## Mypy
+- Updated args so there are no missing imports
+- Updated additional dependencies, so mypy can check all types
+- Note: If the installs in requirements change, it has to be adapted in additional dependencies
+- Added many type annotations
+- In some cases internal refactoring for variables, due to typing
+
+## Pydocstyle and Linter
+- Major overhaul of docstrings in various files
+- Removed unused imports and variables
+
+## Groups
+- Groups now get a default name, if no name was entered by the user.
+- Groups get sorted alphabetically to appear more ordered.
+
+## Additional Changes
+- Added a "make install examples" in Makefile
+
 # Version 1.1.3
 
 ## Bug-Fixes
@@ -24,7 +87,7 @@
 - SMAC 2.0
 
 ## Dependencies
-- Remove SMAC dependency by adding required function directly
+- Remove SMAC dependency by adding required function directly.
 
 # Version 1.0.1
 

Makefile

@@ -2,7 +2,7 @@
 # are usually completed in github actions.
 
 SHELL := /bin/bash
-VERSION := 1.1.3
+VERSION := 1.2
 
 NAME := DeepCAVE
 PACKAGE_NAME := deepcave
@@ -42,13 +42,16 @@ MYPY ?= mypy
 PRECOMMIT ?= pre-commit
 FLAKE8 ?= flake8
 
-install: 
+install:
 	$(PIP) install -e .
 
 install-dev:
 	$(PIP) install -e ".[dev]"
 	pre-commit install
-
+	
+install-examples:
+	$(PIP) install -e ".[examples]"
+	
 check-black:
 	$(BLACK) ${SOURCE_DIR} --check || :
 	$(BLACK) ${EXAMPLES_DIR} --check || :
@@ -62,7 +65,7 @@ check-pydocstyle:
 	$(PYDOCSTYLE) ${SOURCE_DIR} || :
 
 check-mypy:
-	$(MYPY) ${SOURCE_DIR} || :
+	$(MYPY) --check-untyped-defs --install-types --non-interactive --ignore-missing-imports ${SOURCE_DIR} || :
 
 check-flake8:
 	$(FLAKE8) ${SOURCE_DIR} || :
@@ -115,7 +118,7 @@ build:
 # This is done to prevent accidental publishing but provide the same conveniences
 publish: clean build
 	read -p "Did you update the version number in Makefile and deepcave/__init__.py?"
-	
+
 	$(PIP) install twine
 	$(PYTHON) -m twine upload --repository testpypi ${DIST}/*
 	@echo

README.md

@@ -1,3 +1,5 @@
+<img src="docs/images/DeepCAVE_Logo_wide.png" alt="Logo"/> 
+
 # DeepCAVE
 
 DeepCAVE is a visualization and analysis tool for AutoML (especially for the sub-problem
@@ -14,7 +16,7 @@ Following features are provided:
 - A large collection of plugins to explore multiple areas like performance, hyperparameter and
 budget analysis.
 - Save your runs using DeepCAVE's native recorder.
-- Support for many optimizers using converter (e.g., DeepCAVE, SMAC and BOHB).
+- Support for many optimizers using converters (e.g., DeepCAVE, SMAC and BOHB).
 - Select runs directly from a working directory in the interface.
 - Select groups of runs for combined analysis.
 - Modularized plugin structure with access to selected runs/groups to provide maximal flexibility.
@@ -41,12 +43,18 @@ pip install DeepCAVE
 If you want to contribute to DeepCAVE use the following steps instead:
 ```bash
 git clone https://github.com/automl/DeepCAVE.git
+cd DeepCAVE
 conda create -n DeepCAVE python=3.9
 conda activate DeepCAVE
 conda install -c anaconda swig
 make install-dev
 ```
 
+If you want to use the given examples, run this after installing:
+```bash
+make install-examples
+```
+
 Please visit the [documentation](https://automl.github.io/DeepCAVE/main/installation.html) to get
 further help (e.g. if you can not install redis server or you are on a mac).